Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

33886597 .. 33890181

Gene Structure 3585 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG152800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 432 bp

ATGTTCAGATTCAGTCTATATATCCATTGCATGATGTTTCAGAGCTGGAACAAAGGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAACAGGTTGATGATTTGGCATCAAAGGCATGATGTTTCTGAGCTGGAGCAAAAGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAACCCAGATGAGGAGTATGCAGGGGTAGAATCCAGATTGCGTTCACATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCAAGGATATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCAGCTGCCAATCGCTTGTTGGAGGCATATAATGATGCTTTTGAAGGAACGTTGACTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005819 GO:0005856 GO:0005874 GO:0005876 GO:0008017 GO:0008092 GO:0009524 GO:0015630 GO:0015631 GO:0043226 GO:0043228 GO:0043229 GO:0043232 GO:0044422 GO:0044424 GO:0044430 GO:0044444 GO:0044446 GO:0044464 GO:0051011 GO:0099080 GO:0099081 GO:0099512 GO:0099513

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Plant_NMP1

Protein Analysis

143

Amino Acids

16.96

Weight (kDa)

6.37

Isoelectric Point (pI)

51.63

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	41 - 135	6.9e-50	Plant nuclear matrix protein 1 (NMP1)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0000643)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G28230
fragaria_vesca	FvH4_3g16300 FvH4_6g12751 FvH4_6g44570 FvH4_6g44594 FvH4_7g07660
malus_domestica	MD09G1096400.v1.1 MD17G1084500.v1.1
prunus_persica	Prupe.3G231100_v2.0.a1
pyrus_communis	pycom09g02090 pycom17g08160
rosa_chinensis	RchiOBHm_Chr1g0342751 RchiOBHm_Chr2g0157591 RchiOBHm_Chr2g0161781 RchiOBHm_Chr3g0469881
rosa_laevigata	RLG00000007135 RLG00000010298 RLG00000021299 RLG00000021302 RLG00000029173 RLG00000029192
rosa_multiflora	Rmu_sc0000173.1_g000045 Rmu_sc0001403.1_g000033 Rmu_sc0001403.1_g000034 Rmu_sc0001993.1_g000002 Rmu_sc0001993.1_g000020 Rmu_sc0003662.1_g000014 Rmu_sc0011563.1_g000010 Rmu_sc0012276.1_g000010 Rmu_sc0026352.1_g000003
rosa_roxburghii	Rroxscaffold_1G00038970 Rroxscaffold_2G00088610 Rroxscaffold_3G00231870 Rroxscaffold_4G00288710 Rroxscaffold_4G00313230 Rroxscaffold_6G00396080 Rroxscaffold_7G00184860
rosa_rugosa	Rorug01G0146100.1 Rorug02G0491800 Rorug02G0492600 Rorug03G0291200 Rorug05G0303900 Rorug05G0335100 Rorug05G0335200
rosa_samantha	Rh1AG028300 Rh1AG137400 Rh1AG162800 Rh1AG163600 Rh1AG163700 Rh1AG164400 Rh1AG164500 Rh1BG129500 Rh1BG129600 Rh1CG025800 Rh1CG129600 Rh1CG151800 Rh1CG152300 Rh1CG152800 Rh1CG153300 Rh1DG044700 Rh1DG133100 Rh2AG558000 Rh2BG571600 Rh2CG541700 Rh2DG549600 Rh2DG580500 Rh3BG178200 Rh3CG168900 Rh3DG076100 Rh3DG260000 Rh5AG515900 Rh6BG166400 Rh6DG108300 Rh7AG194200 Rh7DG200800 Rh7DG369800
rosa_wichuraiana	Rw2G046170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	349
AccB1I	GGYRCC	1 cut(s)	349
AclI	AACGTT	1 cut(s)	422
AfaI	GTAC	1 cut(s)	351
AfiI	CCNNNNNNNGG	1 cut(s)	229
AgsI	TTSAA	4 cut(s)	91, 182, 301, 416
AjnI	CCWGG	1 cut(s)	329
AluBI	AGCT	5 cut(s)	45, 136, 148, 358, 377
AluI	AGCT	5 cut(s)	45, 136, 148, 358, 377
AoxI	GGCC	1 cut(s)	371
ApeKI	GCWGC	1 cut(s)	377
Asp700I	GAANNNNTTC	1 cut(s)	276
Asp718I	GGTACC	1 cut(s)	349
AspS9I	GGNCC	1 cut(s)	371
BanI	GGYRCC	1 cut(s)	349
BbsI	GAAGAC	2 cut(s)	79, 170
BbvI	GCAGC	1 cut(s)	364
BccI	CCATC	1 cut(s)	337
BciT130I	CCWGG	1 cut(s)	331
BfaI	CTAG	1 cut(s)	281
BisI	GCNGC	1 cut(s)	378
BlsI	GCNGC	1 cut(s)	379
Bme1390I	CCNGG	1 cut(s)	331
BmgT120I	GGNCC	1 cut(s)	371
BmiI	GGNNCC	1 cut(s)	351
BmrFI	CCNGG	1 cut(s)	331
BmsI	GCATC	3 cut(s)	121, 212, 397
BpiI	GAAGAC	2 cut(s)	79, 170
BpmI	CTGGAG	1 cut(s)	158
BpuEI	CTTGAG	2 cut(s)	66, 157
BsaJI	CCNNGG	3 cut(s)	315, 329, 361
BsaXI	ACNNNNNCTCC	2 cut(s)	342, 372
Bsc4I	CCNNNNNNNGG	1 cut(s)	229
Bse3DI	GCAATG	1 cut(s)	25
BseBI	CCWGG	1 cut(s)	331
BseDI	CCNNGG	3 cut(s)	315, 329, 361
BseLI	CCNNNNNNNGG	1 cut(s)	229
BseMI	GCAATG	1 cut(s)	25
BseMII	CTCAG	1 cut(s)	123
BseRI	GAGGAG	1 cut(s)	245
BseXI	GCAGC	1 cut(s)	364
BseYI	CCCAGC	1 cut(s)	354
BshFI	GGCC	1 cut(s)	373
BshNI	GGYRCC	1 cut(s)	349
BslFI	GGGAC	1 cut(s)	312
BslI	CCNNNNNNNGG	1 cut(s)	229
BsmFI	GGGAC	1 cut(s)	312
BsnI	GGCC	1 cut(s)	373
Bsp143I	GATC	1 cut(s)	293
Bsp19I	CCATGG	1 cut(s)	361
BspANI	GGCC	1 cut(s)	373
BspCNI	CTCAG	1 cut(s)	124
BspLI	GGNNCC	1 cut(s)	351
BspT107I	GGYRCC	1 cut(s)	349
BsrDI	GCAATG	1 cut(s)	25
BssECI	CCNNGG	3 cut(s)	315, 329, 361
BssMI	GATC	1 cut(s)	293
BssT1I	CCWWGG	2 cut(s)	315, 361
Bst2UI	CCWGG	1 cut(s)	331
BstC8I	GCNNGC	2 cut(s)	213, 375
BstDEI	CTNAG	1 cut(s)	132
BstDSI	CCRYGG	1 cut(s)	361
BstKTI	GATC	1 cut(s)	296
BstMBI	GATC	1 cut(s)	293
BstMWI	GCNNNNNNNGC	1 cut(s)	118
BstNI	CCWGG	1 cut(s)	331
BstNSI	RCATGY	1 cut(s)	215
BstSCI	CCNGG	1 cut(s)	329
BstV1I	GCAGC	1 cut(s)	364
BstV2I	GAAGAC	2 cut(s)	79, 170
BstXI	CCANNNNNNTGG	1 cut(s)	362
BsuRI	GGCC	1 cut(s)	373
BtgI	CCRYGG	1 cut(s)	361
Cac8I	GCNNGC	2 cut(s)	213, 375
Cfr13I	GGNCC	1 cut(s)	371
Csp6I	GTAC	1 cut(s)	350
CviAII	CATG	5 cut(s)	31, 122, 212, 340, 362
CviJI	RGCY	7 cut(s)	45, 57, 136, 148, 358, 373, 377
CviKI_1	RGCY	7 cut(s)	45, 57, 136, 148, 358, 373, 377
CviQI	GTAC	1 cut(s)	350
DdeI	CTNAG	1 cut(s)	132
DpnI	GATC	1 cut(s)	295
DpnII	GATC	1 cut(s)	293
Eco130I	CCWWGG	2 cut(s)	315, 361
EcoRII	CCWGG	1 cut(s)	329
EcoT14I	CCWWGG	2 cut(s)	315, 361
ErhI	CCWWGG	2 cut(s)	315, 361
FaeI	CATG	5 cut(s)	34, 125, 215, 343, 365
FaqI	GGGAC	1 cut(s)	312
FatI	CATG	5 cut(s)	30, 121, 211, 339, 361
Fnu4HI	GCNGC	1 cut(s)	378
Fsp4HI	GCNGC	1 cut(s)	378
FspBI	CTAG	1 cut(s)	281
GluI	GCNGC	1 cut(s)	378
GsaI	CCCAGC	1 cut(s)	358
GsuI	CTGGAG	1 cut(s)	158
HaeIII	GGCC	1 cut(s)	373
Hin1II	CATG	5 cut(s)	34, 125, 215, 343, 365
HincII	GTYRAC	1 cut(s)	426
HindII	GTYRAC	1 cut(s)	426
HindIII	AAGCTT	1 cut(s)	146
HinfI	GANTC	3 cut(s)	9, 248, 272
Hpy166II	GTNNAC	2 cut(s)	263, 426
Hpy188I	TCNGA	3 cut(s)	8, 42, 133
Hpy188III	TCNNGA	2 cut(s)	252, 281
Hpy8I	GTNNAC	2 cut(s)	263, 426
HpyAV	CCTTC	1 cut(s)	410
HpyCH4IV	ACGT	2 cut(s)	325, 422
HpyCH4V	TGCA	3 cut(s)	30, 239, 290
HpyF10VI	GCNNNNNNNGC	1 cut(s)	118
HpyF3I	CTNAG	1 cut(s)	132
HpySE526I	ACGT	2 cut(s)	325, 422
Hsp92II	CATG	5 cut(s)	34, 125, 215, 343, 365
KpnI	GGTACC	1 cut(s)	353
Kzo9I	GATC	1 cut(s)	293
LmnI	GCTCC	2 cut(s)	139, 363
Lsp1109I	GCAGC	1 cut(s)	364
LweI	GCATC	3 cut(s)	121, 212, 397
MaeI	CTAG	1 cut(s)	281
MaeII	ACGT	2 cut(s)	325, 422
MalI	GATC	1 cut(s)	295
MboI	GATC	1 cut(s)	293
MboII	GAAGA	2 cut(s)	79, 170
MmeI	TCCRAC	1 cut(s)	372
MnlI	CCTC	3 cut(s)	223, 340, 388
MroXI	GAANNNNTTC	1 cut(s)	276
MseI	TTAA	1 cut(s)	430
MspA1I	CMGCKG	1 cut(s)	377
MspR9I	CCNGG	1 cut(s)	331
MvaI	CCWGG	1 cut(s)	331
MwoI	GCNNNNNNNGC	1 cut(s)	118
NcoI	CCATGG	1 cut(s)	361
NdeII	GATC	1 cut(s)	293
NlaIII	CATG	5 cut(s)	34, 125, 215, 343, 365
NlaIV	GGNNCC	1 cut(s)	351
NspI	RCATGY	1 cut(s)	215
PaeI	GCATGC	1 cut(s)	215
PdmI	GAANNNNTTC	1 cut(s)	276
PfeI	GAWTC	3 cut(s)	9, 248, 272
PkrI	GCNGC	1 cut(s)	379
Psp1406I	AACGTT	1 cut(s)	422
Psp6I	CCWGG	1 cut(s)	329
PspFI	CCCAGC	1 cut(s)	354
PspGI	CCWGG	1 cut(s)	329
PspN4I	GGNNCC	1 cut(s)	351
PspPI	GGNCC	1 cut(s)	371
PvuII	CAGCTG	1 cut(s)	377
RsaI	GTAC	1 cut(s)	351
RsaNI	GTAC	1 cut(s)	350
SaqAI	TTAA	1 cut(s)	430
SatI	GCNGC	1 cut(s)	378
Sau3AI	GATC	1 cut(s)	293
Sau96I	GGNCC	1 cut(s)	371
ScrFI	CCNGG	1 cut(s)	331
SfaNI	GCATC	3 cut(s)	121, 212, 397
SmlI	CTYRAG	2 cut(s)	81, 172
SmoI	CTYRAG	2 cut(s)	81, 172
SphI	GCATGC	1 cut(s)	215
SspMI	CTAG	1 cut(s)	281
StyD4I	CCNGG	1 cut(s)	329
StyI	CCWWGG	2 cut(s)	315, 361
TaiI	ACGT	2 cut(s)	328, 425
TfiI	GAWTC	3 cut(s)	9, 248, 272
Tru1I	TTAA	1 cut(s)	430
Tru9I	TTAA	1 cut(s)	430
TseI	GCWGC	1 cut(s)	377
XbaI	TCTAGA	1 cut(s)	280
XceI	RCATGY	1 cut(s)	215
XcmI	CCANNNNNNNNNTGG	1 cut(s)	388
XmnI	GAANNNNTTC	1 cut(s)	276
XspI	CTAG	1 cut(s)	281

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.